strange, i have no micro bubbles that escape the main chamber (i.e. flow back into the tank). I think the carbon cartridge might be helping prevent that.
I only clean the collection cup, and the outflow 'ramp' that dumps into the tank.
Also, I feel like i'm getting a little better collection (darker skimmate) with the pre-filter cup. Just make sure you set it's level so it can't run empty due to evaporation.
Former advisor and planted tank geek...life's moved on though.